The use-agent option is for GnuPG 1.4.x and it means using gpg-agent if available.
If no option, GnuPG 1.4.x directly connects to Gnuk Token by itself, instead of through scdaemon. When GnuPG 1.4.x tries to access Gnuk Token and scdaemon is running, there are conflicts.

We recommend to specify the use-agent option for GnuPG 1.4.x to access Gnuk Token through gpg-agent and scdaemon.

For GnuPG 2.0 and 2.1, gpg-agent is always used, so, there is no need to specify the use-agent option, but having this option is no harm, anyway.